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The good news: The Mississippi River is home to more fish, bald eagles and mussels than in recent history. The bad news: The river is being inundated with more bacteria, phosphates and sediment.

That’s according to the State of the River Report compiled by Friends of the Mississippi River and the National Park Service and funded by the McKnight Foundation, Minnehaha Creek Watershed District and Capitol Region Watershed District.

The report looks at 13 key indicators about the river’s health and water quality, from a Minnesota perspective, but also looks at implications as far south as the Gulf of Mexico.

The report says that increased water flows, brought on by more paved surfaces, rooftops and artificially drained agricultural fields, are eroding river banks, causing floods, destroying habitats and causing pollution.

The median water flow at the Hastings dam has increased by 25 percent since 1976, according to the report.

“A lot of what we’re seeing is flow connected to change in agricultural practices in the upstream portion of out watershed,” said Lark Weller, water quality coordinator for the National Park Service and co-author of the report.

Average bacteria levels are high in the Twin Cities, according to the report, and swimming should be limited and avoided all together within 48 hours of a rainstorm.

The report also highlights a threat that Minneapolis officials, as well as state and federal officials, are trying to deal with. Asian carp appear to be migrating upstream and pose a threat to fisheries in northern Minnesota. None of the carp have been found in the Twin Cities, but officials say they’ve detected them via DNA testing.

The Asian Carp Coalition, of which Friends of the Mississippi River is a member, recommends targeted lock closures at St. Anthony Falls and Lock and Dam No. 1 near the old Ford plant.

That idea has upset the barge industry, which uses the locks to reach industrial sites along the river in North Minneapolis, as well as recreational users who want passage down the river.

“These fish pose such an economic and public safety threat, we feel as though action is warranted,” said Trevor Russell, watershed program director for Friends of the Mississippi River. “What we’re talking about here, with the closure of the Upper St. Anthony Falls Lock and Dam, is essentially restoring the river to its natural biological function allowing the falls to serve … as a natural fish barrier.”

Fortunately for Minneapolis, the city’s residents don’t have to deal with one of the largest problems facing the river, which is increasing loads of sediment from the Minnesota River.

The study says 75 percent of sediment flowing into the metro area comes from the Minnesota River basin, which flows through agriculture-rich southern Minnesota before emptying into the Mississippi River a short distance downriver from Fort Snelling.

Sediment is what makes water appear dirty, but its phosphates also hurt aquatic wildlife and the sediment is filling up Lake Pepin.

The report recommends substantial changes for the Minnesota River basin, including better land use and increased agricultural conservation and water retention.

“We really don’t have the tools to effectively address agricultural runoff, and despite billions invested in voluntary conservation programs over the last two or three decades, that level of increase of a largely agricultural pollutant is stunning and really calls into question whether or not our agricultural pollution control systems are effective,” Russell said.

The report offers a few tips for how residents can help with the problems. Homeowners can install rain gardens, rain barrels, pervious pavers, green roofs and restore prairie landscapes. Residents can also be diligent about cleaning up pet waste and ensuring their septic systems are up-to-date.

For a full list of ways you can help keep the river clean, visit stateoftheriver.com.